Summary of Study ST002395
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001542. The data can be accessed directly via it's Project DOI: 10.21228/M8CM5D This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST002395 |
| Study Title | A Mammalian Conserved Circular RNA CircLARP2 Regulates Hepatocellular Carcinoma Metastasis and Lipid Metabolism (Part 2) |
| Study Summary | Circular RNAs (circRNAs) have emerged as crucial regulators in physiology and human diseases. However, evolutionarily conserved circRNAs with potent functions in cancers are rarely reported. Here, we identified a mammalian conserved circRNA circLARP2 that played critical roles in hepatocellular carcinoma (HCC). With clinical specimens, we found that patients with high circLARP2 levels in HCC had advanced prognostic stage and poor overall survival. CircLARP2 facilitated HCC metastasis and lipid accumulation in HCC cell lines. CircLARP2 was one of the rare ones that were identified in HCC metastasis and conserved in mammals, which enabled further studies with animal models. CircLARP2-deficient mice exhibited reduced metastasis and less lipid accumulation in an induced HCC model. We provided lines of evidence at molecular, cellular, and whole organismal levels, to support that circLARP2 functioned as a protein sponge of AUF1. CircLARP2 sequestered AUF1 from binding to LKB1 mRNA, which led to decreased LKB1 mRNA stability and lower LKB1 protein levels. LKB1 as a kinase promoted the phosphorylation of AMPK and then the phosphorylation of ACC, the rate limiting enzyme of fatty acid synthesis. Knockdown of Lkb1 with AAV8-shLkb1 in mice HCC model also proved that Lkb1 was a key element in the regulation. Through this AUF1-LKB1-AMPK-ACC pathway, circLARP2 promoted HCC metastasis and lipid accumulation. |
| Institute | University of Science and Technology of China |
| Last Name | Li |
| First Name | Jingxin |
| Address | 443 Huangshan Road, HeFei, AnHui, 230022, China |
| ljx0418@mail.ustc.edu.cn | |
| Phone | 00-86-0551-63600137 |
| Submit Date | 2023-03-10 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-04-06 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001542 |
| Project DOI: | doi: 10.21228/M8CM5D |
| Project Title: | A Mammalian Conserved Circular RNA CircLARP2 Regulates Hepatocellular Carcinoma Metastasis and Lipid Metabolism |
| Project Summary: | Circular RNAs (circRNAs) have emerged as crucial regulators in physiology and human diseases. However, evolutionarily conserved circRNAs with potent functions in cancers are rarely reported. Here, we identified a mammalian conserved circRNA circLARP2 that played critical roles in hepatocellular carcinoma (HCC). With clinical specimens, we found that patients with high circLARP2 levels in HCC had advanced prognostic stage and poor overall survival. CircLARP2 facilitated HCC metastasis and lipid accumulation in HCC cell lines. CircLARP2 was one of the rare ones that were identified in HCC metastasis and conserved in mammals, which enabled further studies with animal models. CircLARP2-deficient mice exhibited reduced metastasis and less lipid accumulation in an induced HCC model. We provided lines of evidence at molecular, cellular, and whole organismal levels, to support that circLARP2 functioned as a protein sponge of AUF1. CircLARP2 sequestered AUF1 from binding to LKB1 mRNA, which led to decreased LKB1 mRNA stability and lower LKB1 protein levels. LKB1 as a kinase promoted the phosphorylation of AMPK and then the phosphorylation of ACC, the rate limiting enzyme of fatty acid synthesis. Knockdown of Lkb1 with AAV8-shLkb1 in mice HCC model also proved that Lkb1 was a key element in the regulation. Through this AUF1-LKB1-AMPK-ACC pathway, circLARP2 promoted HCC metastasis and lipid accumulation. |
| Institute: | University of Science and Technology of China |
| Last Name: | Li |
| First Name: | Jingxin |
| Address: | 443 Huangshan Road |
| Email: | ljx0418@mail.ustc.edu.cn |
| Phone: | 00-86-0551-63600137 |
Subject:
| Subject ID: | SU002602 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype |
|---|---|---|
| SA251716 | KO-2 | circLARP2-deficiency |
| SA251717 | KO-3 | circLARP2-deficiency |
| SA251718 | KO-1 | circLARP2-deficiency |
| SA251713 | WT-3 | Wild-type |
| SA251714 | WT-2 | Wild-type |
| SA251715 | WT-1 | Wild-type |
| Showing results 1 to 6 of 6 |
Collection:
| Collection ID: | CO002595 |
| Collection Summary: | 500 μL cold extraction buffer (methanol: acetonitrile: water = 2:2:1, v/v/v) was added to each sample. Samples were sonicated for 2 minutes and centrifuged at 14,000 g for 5 min at 4 °C. Supernatants were thoroughly lyophilized (FreeZone 6 Liter, Labconco, USA) and reconstituted in 50 μL of methanol-water (1:1, v/v) just prior to measurement. |
| Sample Type: | Cultured cells |
Treatment:
| Treatment ID: | TR002614 |
| Treatment Summary: | Twenty-four hours after seeding, cells were washed three times with 0.9% NaCl and incubated in DMEM without glucose, glutamine or sodium pyruvate supplemented with 15 mM [U-13C] glucose, 4 mM [U-13C] glutamine, 10% FBS and the indicated treatment condition for 24 h before metabolite extraction. |
Sample Preparation:
| Sampleprep ID: | SP002608 |
| Sampleprep Summary: | Supernatants were thoroughly lyophilized (FreeZone 6 Liter, Labconco, USA) and reconstituted in 50 μL of methanol-water (1:1, v/v) just prior to measurement. |
Combined analysis:
| Analysis ID | AN004119 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Vanquish |
| Column | SeQuant ZIC-HILIC (100 x 2.1mm,3.5um) |
| MS Type | ESI |
| MS instrument type | Triple TOF |
| MS instrument name | Thermo Q Exactive Plus Orbitrap |
| Ion Mode | POSITIVE |
| Units | peak area |
Chromatography:
| Chromatography ID: | CH003051 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | SeQuant ZIC-HILIC (100 x 2.1mm,3.5um) |
| Column Temperature: | 45 |
| Flow Gradient: | The initial mobile phase was 30% solvent B at a flow rate of 300 μL/min. It was held for 2 min, and then linearly increased to 100% solvent B in 23 min, followed by equilibrating at 5% solvent B for 10 min. |
| Flow Rate: | 300 μL/min |
| Solvent A: | acetonitrile–water (6:4, v/v) with 0.1% formic acid and 0.1mM ammonium formate |
| Solvent B: | acetonitrile–isopropanol (1:9, v/v) with 0.1% formic acid and 0.1 mM ammonium formate |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS003866 |
| Analysis ID: | AN004119 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Triple TOF |
| MS Type: | ESI |
| MS Comments: | Data processing and ion annotation based on accurate mass were performed in TraceFinder 5.0 (Thermo Fisher) and Xcalibur 4.0 (Thermo Fisher). |
| Ion Mode: | POSITIVE |
